Abstract: The submarine cold seeps are closely related to some important scientific issues, such as the occurrence of natural gas hydrate, global climate change, and extreme environmental ecosystems. There are many factors affecting the formation and evolution of cold seep systems. Their spatial and temporal distribution, activity characteristics, and related physical, chemical, and biological effects are very different from place to place. The coupling relationship between shallow surface cold seeps activities and their deep controlling factors, the hydrodynamic process and control mechanism of differential development of cold seeps need to be further studied. This paper tries to take the Qiongdongnan Basin as the research object and select some typical cold seep active stations as cases to solve the problem of cold seep differential activity process and their control mechanisms. Based on previous researches, taken the hydrodynamic research as the key, and combined the observation data of shallow cold seeps together with the deep geological environment and formation pressure, some numerical models are set up in this paper for the cold seep fluid flow and energy conversion process. The dynamics process of fluid migration from deep to shallow are portrayed. And analyzed are also the geological conditions and control factors for different cold seep systems. Afterward, the coupling relationship between the shallow surface responses of cold seeps to the deep elements is identified. Then a dynamic model of cold seep differential development is established. In the end, the control mechanisms of cold seep differentiation are discussed. This work may provide a theoretical basis for hydrate exploration and trial mining, study of deep-sea material and energy migration and transformation, and research of the extreme environmental ecosystem of cold seep.